Hello,
I am trying to use parallelism in Galaxy. I added this entry to the tool xml config:
<tool id="fa_gc_content_1" name="Compute GC content">
<description>for each sequence in a file</description>
<parallelism method="basic" split_size="8" split_mode="number_of_parts"></parallelism>
But when I run the job, the log shows the next:
Traceback (most recent call last):
File "/home/ralonso/galaxy-dist/lib/galaxy/jobs/runners/__init__.py", line 158, in prepare_job
job_wrapper.prepare()
File "/home/ralonso/galaxy-dist/lib/galaxy/jobs/__init__.py", line 1607, in prepare
tool_evaluator.set_compute_environment( compute_environment )
File "/home/ralonso/galaxy-dist/lib/galaxy/tools/evaluation.py", line 53, in set_compute_environment
incoming = self.tool.params_from_strings( incoming, self.app )
File "/home/ralonso/galaxy-dist/lib/galaxy/tools/__init__.py", line 2810, in params_from_strings
return params_from_strings( self.inputs, params, app, ignore_errors )
File "/home/ralonso/galaxy-dist/lib/galaxy/tools/parameters/__init__.py", line 103, in params_from_strings
value = params[key].value_from_basic( value, app, ignore_errors )
File "/home/ralonso/galaxy-dist/lib/galaxy/tools/parameters/basic.py", line 162, in value_from_basic
return self.to_python( value, app )
File "/home/ralonso/galaxy-dist/lib/galaxy/tools/parameters/basic.py", line 1999, in to_python
return app.model.context.query( app.model.HistoryDatasetAssociation ).get( int( value ) )
File "/home/ralonso/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py", line 775, in get
return self._load_on_ident(key)
File "/home/ralonso/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py", line 2512, in _load_on_ident
return q.one()
File "/home/ralonso/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py", line 2184, in one
ret = list(self)
File "/home/ralonso/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py", line 2227, in __iter__
return self._execute_and_instances(context)
File "/home/ralonso/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py", line 2242, in _execute_and_instances
result = conn.execute(querycontext.statement, self._params)
File "/home/ralonso/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 1449, in execute
params)
File "/home/ralonso/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 1584, in _execute_clauseelement
compiled_sql, distilled_params
File "/home/ralonso/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 1698, in _execute_context
context)
File "/home/ralonso/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 1691, in _execute_context
context)
File "/home/ralonso/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/default.py", line 331, in do_execute
cursor.execute(statement, parameters)
OperationalError: (OperationalError) database is locked u'SELECT
history_dataset_association.id AS history_dataset_association_id, history_dataset_association.history_id AS history_dataset_association_history_id, history_dataset_association.dataset_id AS history_dataset_association_dataset_id, history_dataset_association.create_time AS history_dataset_association_create_time, history_dataset_association.update_time AS history_dataset_association_update_time, history_dataset_association.state AS history_dataset_association_state, history_dataset_association.copied_from_history_dataset_association_id AS history_dataset_association_copied_from_history_dataset_association_id, history_dataset_association.copied_from_library_dataset_dataset_association_id AS history_dataset_association_copied_from_library_dataset_dataset_association_id, history_dataset_association.hid AS history_dataset_association_hid,
history_dataset_association.name AS history_dataset_association_name,
history_dataset_association.info AS history_dataset_association_info, history_dataset_association.blurb AS history_dataset_association_blurb, history_dataset_association.peek AS history_dataset_association_peek, history_dataset_association.tool_version AS history_dataset_association_tool_version, history_dataset_association.extension AS history_dataset_association_extension, history_dataset_association.metadata AS history_dataset_association_metadata, history_dataset_association.parent_id AS history_dataset_association_parent_id, history_dataset_association.designation AS history_dataset_association_designation, history_dataset_association.deleted AS history_dataset_association_deleted, history_dataset_association.purged AS history_dataset_association_purged, history_dataset_association.visible AS history_dataset_association_visible, history_dataset_association.hidden_beneath_collection_instance_id AS history_dataset_association_hidden_beneath_collection_instance_id, history_dataset_association.extended_metadata_id AS history_dataset_association_extended_metadata_id,
dataset_1.id AS dataset_1_id, dataset_1.create_time AS dataset_1_create_time, dataset_1.update_time AS dataset_1_update_time, dataset_1.state AS dataset_1_state, dataset_1.deleted AS dataset_1_deleted, dataset_1.purged AS dataset_1_purged, dataset_1.purgable AS dataset_1_purgable, dataset_1.object_store_id AS dataset_1_object_store_id, dataset_1.external_filename AS dataset_1_external_filename, dataset_1._extra_files_path AS dataset_1__extra_files_path, dataset_1.file_size AS dataset_1_file_size, dataset_1.total_size AS dataset_1_total_size, dataset_1.uuid AS dataset_1_uuid \nFROM history_dataset_association LEFT OUTER JOIN dataset AS dataset_1 ON
dataset_1.id = history_dataset_association.dataset_id \nWHERE
history_dataset_association.id = ?' (1,)
galaxy.jobs.runners ERROR 2015-02-05 12:58:11,431 (89_486) Failure preparing job
So when one task tries to run it fails, it seems that the database is locked by other task. When I run with 4 splits it never happen, but with 5 it begins to happen. Indeed with 5 splits sometimes it doesn't happen, but since 6 it always occurs.
Could you please help me?
Regards